Last updated: 2022-10-22

Checks: 6 1

Knit directory: factor_analysis/

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Rmd ae43c9c XSun 2022-10-21 update
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html 0706c05 XSun 2022-10-17 update

Introduction

Workflow:

  1. Association test: factor ~ snp + covariates

  2. For the pairs have multiple snps passing FDR < 0.2, do ECT

Results

The number of SNPs passing FDR < 0.2 in association tests

Version Author Date
ae43c9c XSun 2022-10-21
0706c05 XSun 2022-10-17

ECT results

Number of pairs passing different ECT FDR cutoff

Version Author Date
ae43c9c XSun 2022-10-21
0706c05 XSun 2022-10-17

ECT qqplots and rsq barplots for all pairs have >=3SNPs

Version Author Date
ae43c9c XSun 2022-10-21
0706c05 XSun 2022-10-17

Version Author Date
ae43c9c XSun 2022-10-21
0706c05 XSun 2022-10-17

ECT qqplots and rsq barplots for all pairs have >=5SNPs

Version Author Date
ae43c9c XSun 2022-10-21

Version Author Date
ae43c9c XSun 2022-10-21

Top 10 pairs have ECT FDR <0.1

effect size plots for the top 2 pairs

Version Author Date
ae43c9c XSun 2022-10-21

Version Author Date
ae43c9c XSun 2022-10-21

Detailed results

B cell (CD19+)

Compute ECT FDR only for pairs have >=5 SNPs

Monocyte (CD14+)

Compute ECT FDR only for pairs have >=5 SNPs

Leukocyte (CD15+)

Compute ECT FDR only for pairs have >=5 SNPs

Platelet

Compute ECT FDR only for pairs have >=5 SNPs

T cell (CD4+)

Compute ECT FDR only for pairs have >=5 SNPs

T cell (CD8+)

Compute ECT FDR only for pairs have >=5 SNPs


sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.3.13-el7-x86_64/lib/libopenblas_haswellp-r0.3.13.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] forcats_0.5.1 tidyr_1.2.0   gridExtra_2.3 ggplot2_3.3.5

loaded via a namespace (and not attached):
 [1] tidyselect_1.1.2  xfun_0.30         bslib_0.3.1       purrr_0.3.4      
 [5] lattice_0.20-45   splines_4.2.0     colorspace_2.0-3  vctrs_0.4.1      
 [9] generics_0.1.2    htmltools_0.5.2   mgcv_1.8-40       yaml_2.3.5       
[13] utf8_1.2.2        rlang_1.0.5       jquerylib_0.1.4   later_1.3.0      
[17] pillar_1.7.0      glue_1.6.2        withr_2.5.0       DBI_1.1.2        
[21] lifecycle_1.0.1   stringr_1.4.0     munsell_0.5.0     gtable_0.3.0     
[25] workflowr_1.7.0   htmlwidgets_1.5.4 evaluate_0.15     labeling_0.4.2   
[29] knitr_1.39        fastmap_1.1.0     crosstalk_1.2.0   httpuv_1.6.5     
[33] fansi_1.0.3       highr_0.9         Rcpp_1.0.8.3      DT_0.22          
[37] promises_1.2.0.1  scales_1.2.0      jsonlite_1.8.0    farver_2.1.0     
[41] fs_1.5.2          digest_0.6.29     stringi_1.7.6     dplyr_1.0.9      
[45] grid_4.2.0        rprojroot_2.0.3   cli_3.3.0         tools_4.2.0      
[49] magrittr_2.0.3    sass_0.4.1        tibble_3.1.7      crayon_1.5.1     
[53] whisker_0.4       pkgconfig_2.0.3   Matrix_1.4-1      ellipsis_0.3.2   
[57] assertthat_0.2.1  rmarkdown_2.14    rstudioapi_0.13   R6_2.5.1         
[61] nlme_3.1-157      git2r_0.30.1      compiler_4.2.0